|
| Status |
Public on Jun 30, 2017 |
| Title |
CCT rep1 |
| Sample type |
SRA |
| |
|
| Source name |
Chin competent telogen skin 1
|
| Organism |
Mus musculus |
| Characteristics |
tissue: skin
strain: C57BL/6
tissue location: chin
hair cycle stage: competent telogen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated using the RNEasy Mini-Kit (Qiagen) as per manufacturer’s protocol with minor modifications (Qiagen). Optimal-quality RNAs were considered for cDNA library preparation (RIN>8.0).
100ng total RNA was reversed-transcribed, and resulting cDNA was pre-amplified for 10 cycles. Tagmentation was carried out on 10ng cDNA using the Nextera DNA Sample Preparation Kit (Illumina). The tagmentation reaction was carried out at 55°C for 5 minutes and purified using PCR Purification Kit (Qiagen). Transposed cDNA was utilized for limited cycle enrichment PCR using v2_Adx.x barcodes (IDT). Libraries were amplified for 12 continuous cycles and resulting libraries were purified with AMPure XP beads (Beckman Coulter). Library quantification was done using KAPA for Illumina Sequencing Platforms (Illumina)
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
protocol: SMART-seq2
processed data file: Skin_domains_RNAseq_fpkm.txt
|
| Data processing |
RSEM was used for alignment, mapping and quantification
Reads were not trimmed for adaptor sequence. Sequenced reads were aligned, mapped and quantified to the mouse genome (mm10/vM4) using RSEM v1.2.25 with standard parameters. (B. Li, C. N. Dewey, RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC bioinformatics 12, 323 (2011).).
Genome_build: Gencode vM8
Supplementary_files_format_and_content: tab-delimited text files include FPKM values for each Sample
|
| |
|
| Submission date |
Aug 01, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Maksim V Plikus |
| E-mail(s) |
plikus@uci.edu
|
| Phone |
949-824-1260
|
| Organization name |
University of California, Irvine
|
| Department |
Developmental and Cell Biology
|
| Street address |
845 Health Sciences Road
|
| City |
Irvine |
| State/province |
California |
| ZIP/Postal code |
92697 |
| Country |
USA |
| |
|
| Platform ID |
GPL19057 |
| Series (1) |
| GSE85039 |
A multi-scale model for hair follicle reveals heterogeneous skin domains drive rapid spatiotemporal hair growth patterning |
|
| Relations |
| BioSample |
SAMN05468289 |
| SRA |
SRX1992985 |
